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55 lines
1.7 KiB
Text
55 lines
1.7 KiB
Text
//
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// Create Krona visualizations
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//
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include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/modules/krakentools/kreport2krona/main'
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include { KRONA_CLEANUP } from '../../modules/local/krona_cleanup'
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include { KRONA_KTIMPORTTEXT } from '../../modules/nf-core/modules/krona/ktimporttext/main'
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workflow VISUALIZATION_KRONA {
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take:
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profiles
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main:
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ch_krona_text = Channel.empty()
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ch_krona_html = Channel.empty()
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ch_versions = Channel.empty()
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/*
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Split profile results based on tool they come from
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*/
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ch_input_profiles = profiles
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.branch {
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kraken2: it[0]['tool'] == 'kraken2'
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unknown: true
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}
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/*
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Convert Kraken2 formatted reports into Krona text files
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*/
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ch_kraken_reports = ch_input_profiles.kraken2
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KRAKENTOOLS_KREPORT2KRONA ( ch_kraken_reports )
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ch_krona_text = ch_krona_text.mix( KRAKENTOOLS_KREPORT2KRONA.out.txt )
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ch_versions = ch_versions.mix( KRAKENTOOLS_KREPORT2KRONA.out.versions.first() )
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/*
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Remove taxonomy level annotations from the Krona text files
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*/
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KRONA_CLEANUP( ch_krona_text )
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ch_cleaned_krona_text = KRONA_CLEANUP.out.txt
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ch_versions = ch_versions.mix( KRONA_CLEANUP.out.versions.first() )
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/*
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Convert Krona text files into html Krona visualizations
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*/
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ch_krona_text_for_import = ch_cleaned_krona_text
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.map{[[id: it[0]['db_name']], it[1]]}
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.groupTuple()
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KRONA_KTIMPORTTEXT( ch_krona_text_for_import )
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ch_krona_html = ch_krona_html.mix( KRONA_KTIMPORTTEXT.out.html )
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ch_versions = ch_versions.mix( KRONA_KTIMPORTTEXT.out.versions.first() )
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emit:
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html = ch_krona_html
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versions = ch_versions
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}
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